Characterization of the complete mitochondrial genome and phylogenetic relationship of Pomatorhinus ruficollis (Passeriformes, Timaliinae)

Abstract

In our study, we first report complete mitogenome for P. ruficollis and obtain basic genetic information. The genome of P. ruficollis is 17 009 bp which contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. Overall bases composition of the complete mitochondrial genome is 29.70%A, 14.47%G, 23.31% T, 32.52%C. Twelve PCGs and 14 tRNA genes are distributed on the H-strand, ND6 and eight tRNA genes are encoded on the L-strand.

Keywords:

• Mitochondrial genome
• Pomatorhinus
• Pomatorhinus ruficollis

Pomatorhinus ruficollis (Rufous-necked scimitar babbler) is one of the members in Pomatorhinus genus, they distributed in northern Indochina, northern and western Burma, central to southern China and sino-Himalayan. Pomatorhinus rufillos are mainly live in lowlands, foothills and montane forests (Nyari & Reddy 2013) range altitude from 200 m to 3000 m (Song et al. 2011). The population of P. ruficollis sudden drop due to e-waste polluted (Zhang et al. 2015). Because P. ruficollis chest differ in the colours spots, vertical lines and it can be slipted into at least three groups (Cheng 1964; Collar 2006; Collar & Robson 2007). Based on the morphological characteristics of P. rufillos includes 14 subspecies (Cheng 1962). P.r. musicus is promoted to be independent specie with morphometric differences (Collar 2004, 2006). Therefore, P. ruficollis contains 13 subspecies (Song et al. 2011). The complete mitochondrial genome of P.ruficollis will be helpful for the deeply study on the genetic phylogeny and can provided the method for species conservation.

In our experiment, the muscle sample of P. ruficollis was collected from Ya'an (N30°01', E103°02') and stored at the Wildlife Conservation Laboratory, Sichuan Agricultural University, Sichuan province, China. The mitochondrial genome extracted from the muscle tissue by phenol-chloroform method (Sambrook & Russell 2001). We designed 21 pairs of normal PCR primers and four pairs LA-PCR primers by primer 5.0 according to complete mitochondrial genome of Garrulax cineraceus (GeneBank accession no. NC024553). MAGE6.0 (Tamura et al., 2013) is used to construct neighbour-joining (NJ) tree.

The complete mitogenome of P. ruficollis is 17 009 bp submitted to GenBank (KT970675). The mitogenome have 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and two control regions (D-loop). Twelve PCGs and 14 tRNA are distributed on the H-strand, ND6 and eight tRNA genes are encoded on the L-strand. The base composition of mitogenome is 29.70%A, 14.47%G, 23.31% T and 32.52%C, so the percentage of A + T (53.01%) is slightly higher than G + C (46.99%). Twelve of the 13 protein-coding genes regard ATG as start codon, except GTG for ND1 gene. Four PCGs (ND2, COX3, ND3 and ND4) showed incomplete stop codons (T or TA), the five genes (COX2, ATP8, ATP6, ND4 and Cytb) end with TAA, ND1 and ND5 stops with AGA, COX1 use AGG, and ND6 terminated with TGA. Twelve SrRNA and 16 SrRNA are located between tRNA^Phe and tRNA^Leu(UUR) that is separated by tRNA^Val, with the size of 982 and 1601 bp, respectively. The two control regions (CR) of the P. ruficollis are 1058 bp and 385 bp, CR1 is located between the tRNA^Thr and tRNA^Pro and CR2 between tRNA^Glu and tRNA^Phe. Pomatorhinus ruficollis complete mitochondrial genome structure is similar to the typical mitochondrial genomse of vertebrates (Qian et al. 2012; Zhang et al. 2013; Duan et al. 2014).

Figure 1 shows that Pomatorhinus genus gathered to one clade, Xiphirhynchus superciliaris and Pomatorhinus ferruginosus are clustered as a sister lineage. Pomatorhinus is not monophyly, which is consistent with other studies (Cibois 2003; Collar 2004; Reddy & Moyle 2010; Moyle et al. 2012).

Figure 1. The phylogenetic tree used the method of neighbour-joining (NJ) tree based on ND2, ND3, Cytb protein-coding genes with Kimura 2-parameter model by using MEGA 6.0 program (MEGA Inc., Englewood, NJ). The number on each branch indicated the local bootstrap value. The ND2, ND3 and Cytb Genebank accession number are arranged in brackets after the name of the species.

Disclosure statement

This work was supported by the National Natural Science Foundation of China (31370407). The authors report no conflicts of interest, and are alone responsible for the content and writing of the paper.